NCLscan: accurate identification of non-co-linear transcripts (fusion,trans-splicing and circular RNA) with a good balance between sensitivity and precision

The RNA Binding Protein Quaking Regulates Formation of circRNAs

(2015) Simon J. Conn et al.   CELL

Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals

(2015) Andranik Ivanov et al.   Cell Reports

Biogenesis, identification, and function of exonic circular RNAs

(2015) Iju Chen et al.   Wiley Interdisciplinary Reviews-RNA

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

(2015) Yuan Gao et al.   GENOME BIOLOGY

Correlation of circular RNA abundance with proliferation – exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis and normal human tissues

(2015) Anna Bachmayr-Heyda et al.   Scientific Reports

Complementary Sequence-Mediated Exon Circularization

(2014) Xiao-Ou Zhang et al.   CELL

The Landscape of MicroRNA, Piwi-Interacting RNA, and Circular RNA in Human Saliva

(2014) J. H. Bahn et al.   CLINICAL CHEMISTRY

Detecting and characterizing circular RNAs

(2014) William R Jeck et al.   NATURE BIOTECHNOLOGY

Is an observed non-co-linear RNA product spliced intrans, incisor justin vitro?

(2014) Chun-Ying Yu et al.   NUCLEIC ACIDS RESEARCH

ChiTaRS 2.1—an improved database of the chimeric transcripts and RNA-seq data with novel sense–antisense chimeric RNA transcripts

(2014) Milana Frenkel-Morgenstern et al.   NUCLEIC ACIDS RESEARCH

Circular RNA Is Expressed across the Eukaryotic Tree of Life

(2014) Peter L. Wang et al.   PLoS One

circBase: a database for circular RNAs

(2014) Petar Glažar et al.   RNA

Circular RNAs: diversity of form and function

(2014) Erika Lasda et al.   RNA

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

(2014) Jakub O. Westholm et al.   Cell Reports

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq

(2013) Chenglin Liu et al.   BMC BIOINFORMATICS

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

(2013) Matteo Carrara et al.   BMC BIOINFORMATICS

Circular RNAs: splicing’s enigma variations

(2013) Matthias W Hentze et al.   EMBO JOURNAL

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency

(2013) C.-S. Wu et al.   GENOME RESEARCH

The Atypical Guanine Nucleotide Exchange Factor Dock4 Regulates Neurite Differentiation through Modulation of Rac1 GTPase and Actin Dynamics

(2013) Yangui Xiao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity

(2013) Matteo Carrara et al.   Biomed Research International

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

(2013) Wenlong Jia et al.   GENOME BIOLOGY

CRAC: an integrated approach to the analysis of RNA-seq reads

(2013) Nicolas Philippe et al.   GENOME BIOLOGY

Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model

(2012) F. Abate et al.   BIOINFORMATICS

Novel domain combinations in proteins encoded by chimeric transcripts

(2012) Milana Frenkel-Morgenstern et al.   BIOINFORMATICS

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

(2012) K. Chen et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Chimeric RNAs as potential biomarkers for tumor diagnosis

(2012) Jianhua Zhou et al.   BMB Reports

Identification and analysis of pig chimeric mRNAs using RNA sequencing data

(2012) Lei Ma et al.   BMC GENOMICS

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials

(2012) M. Tang et al.   HAEMATOLOGICA

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery

(2012) Rocco Piazza et al.   NUCLEIC ACIDS RESEARCH

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

(2012) Julia Salzman et al.   PLoS One

FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data

(2012) Richard W. Francis et al.   PLoS One

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

(2012) Onur Sakarya et al.   PLoS Computational Biology

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq

(2011) Yang Li et al.   BIOINFORMATICS

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

(2011) Gregory R. Grant et al.   BIOINFORMATICS

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

(2011) Huanying Ge et al.   BIOINFORMATICS

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

A novel and well-defined benchmarking method for second generation read mapping

(2011) Manuel Holtgrewe et al.   BMC BIOINFORMATICS

Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines

(2011) Kevin CH Ha et al.   BMC Medical Genomics

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

(2011) Serban Nacu et al.   BMC Medical Genomics

Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant

(2011) H. H. Al-Balool et al.   GENOME RESEARCH

Transcriptional consequences of genomic structural aberrations in breast cancer

(2011) K. Inaki et al.   GENOME RESEARCH

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

(2011) Adam J Bass et al.   NATURE GENETICS

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

(2011) Henrik Edgren et al.   GENOME BIOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

Characterization of a Family with Rare Deletions in CNTNAP5 and DOCK4 Suggests Novel Risk Loci for Autism and Dyslexia

(2010) Alistair T. Pagnamenta et al.   BIOLOGICAL PSYCHIATRY

The transcriptional interactome: gene expression in 3D

(2010) Stefan Schoenfelder et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

(2010) Jonathan Houseley et al.   PLoS One

Global analysis of trans-splicing in Drosophila

(2010) C. J. McManus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SLC45A3-ELK4 Is a Novel and Frequent Erythroblast Transformation-Specific Fusion Transcript in Prostate Cancer

(2009) D. S. Rickman et al.   CANCER RESEARCH

High-density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L–DOCK4 gene region in autism susceptibility

(2009) E Maestrini et al.   MOLECULAR PSYCHIATRY

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Implications of chimaeric non-co-linear transcripts

(2009) Thomas R. Gingeras   NATURE

ChimerDB 2.0—a knowledgebase for fusion genes updated

(2009) Pora Kim et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line

(2009) Qi Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck

(2009) M. Persson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosomal Abnormalities in Cancer

(2008) Stefan Fröhling et al.   NEW ENGLAND JOURNAL OF MEDICINE

A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells

(2008) H. Li et al.   SCIENCE